Gene Expression and Coexpression Alterations Marking Evolution of Bladder Cancer
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Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Identification of 10 Important Genes with Poor Prognosis in Non-Small Cell Lung Cancer Through Bioinformatical Analysis
Journal of ISSN: 2581-7388 Inno Biomedical Research and Reviews Volume 3: 2 J Biomed Res Rev 2020 Identification of 10 Important Genes with Poor Prognosis in Non-Small Cell Lung Cancer through Bioinformatical Analysis Wenbin Wu†1 1Experiment Animal Center, Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, PR China †2,3 Cheng Fang 2Center for Traditional Chinese Medicine and Immunology Research, Shanghai University of Traditional Chinese Medicine, PR China Chaochao Zhang1 3Department of Immunology and Pathogenic Biology, School of Basic Medical Nanhua Hu*4 Sciences, Shanghai University of Traditional Chinese Medicine, PR China 4Department of Hepatopancreatobiliary and Traditional Chinese Medicine, Minhang *2,3 Lixin Wang Branch, Fudan University Shanghai Cancer Center, PR China † These authors contributed equally to this work Abstract Article Information Objective: The lung cancer has become the most lethal cause of Article Type: Research Article cancer-related death in China and is responsible for more than 1 million Article Number: JBRR-143 deaths all over the world every year, especially non-small cell lung cancer Received Date: 16 October, 2020 (NSCLC). Although great advance in pharmaceutical therapies for lung Accepted Date: 11 November, 2020 Published Date: 18 November, 2020 the effective biomarkers in order to improve and predict the prognosis ofcancer lung patients, cancer patients.the overall The survival integrated is still bioinformaticalpoor. It is necessary analysis, to find as out a *Corresponding author: Lixin Wang, Center for useful tool to dig up the valuable clues, can be applied to search new Traditional Chinese Medicine and Immunology Research; effective therapeutic targets. -
The Role of E2F7 and E2F8 in Squamous Differentiation, UV- and Chemotherapy-Induced Responses in Keratinocytes
The role of E2F7 and E2F8 in squamous differentiation, UV- and chemotherapy-induced responses in keratinocytes Mehlika Hazar Rethinam MScBiotech (Hons) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2014 UQ Diamantina Institute i Abstract Among keratinocyte-derived squamous cell carcinoma (SCC), cutaneous SCC (CSCC) is the second most common cutaneous cancer type and the most common of the potentially fatal skin cancers. Approximately 90% of head and neck cancers are SCC (HNSCC) and HNSCC worldwide is the sixth most common cancer type afflicting mankind. While resectable disease may be treated by surgery with radiation or chemoradiation, there are still no curative options for advanced, unresectable disease. However, chemotherapy alone may offer a hope for unresectable, disseminated SCC, where 50-60% of patients have disease recurrence within 2 years and approximately 30% of these develop metastatic disease. The mainstay of chemotherapeutic treatment in SCC is the platinum-based drug, cisplatin, 5-fluorouracil (5- FU), taxanes, and anti-EGFR monoclonal antibody such as Cetuximab. Nonetheless, despite advances in treatment techniques, the 5-year survival rate still remains at around 55%. Therefore, there remains a lack of options for recurrent or metastatic disease. The E2F family of transcription factors has emerged as key regulators of proliferation, differentiation and response to stress and apoptotic stimuli in keratinocytes. Consistent with these roles, dysregulation of E2F expression/activity is a common occurrence in cancer and SCC in particular. Thus, better understanding of the E2F family of proteins is essential to establish how these processes are disrupted during SCC genesis. -
Molecular Dynamics and Evolutionary Aspects of the Transition from the Fully Grown Oocyte to Embryo
Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo Alexei V. Evsikov,1,5 Joel H. Graber,1 J. Michael Brockman,1,2 Aleš Hampl,3 Andrea E. Holbrook,1 Priyam Singh,1,2 John J. Eppig,1 Davor Solter,1,4 and Barbara B. Knowles1 1The Jackson Laboratory, Bar Harbor, Maine 04609, USA; 2 Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; 3Masaryk University Brno and Institute of Experimental Medicine, 625 00 Brno, Czech Republic; 4Max Planck Institute of Immunobiology, 79108 Freiburg, Germany Fully grown oocytes (FGOs) contain all the necessary transcripts to activate molecular pathways underlying the oocyte-to-embryo transition (OET). To elucidate this critical period of development, an extensive survey of the FGO transcriptome was performed by analyzing 19,000 expressed sequence tags of the Mus musculus FGO cDNA library. Expression of 5400 genes and transposable elements is reported. For a majority of genes expressed in mouse FGOs, homologs transcribed in eggs of Xenopus laevis or Ciona intestinalis were found, pinpointing evolutionary conservation of most regulatory cascades underlying the OET in chordates. A large proportion of identified genes belongs to several gene families with oocyte-restricted expression, a likely result of lineage-specific genomic duplications. Gene loss by mutation and expression in female germline of retrotransposed genes specific to M. musculus is documented. These findings indicate rapid diversification of genes involved in female reproduction. Comparison of the FGO and two-cell embryo transcriptomes demarcated the processes important for oogenesis from those involved in OET and identified novel motifs in maternal mRNAs associated with transcript stability. -
Identification of Novel Biomarkers and Candidate Small Molecule Drugs in Non-Small-Cell Lung Cancer by Integrated Microarray Analysis
OncoTargets and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis This article was published in the following Dove Press journal: OncoTargets and Therapy Qiong Wu1,2,* Background: Non-small-cell lung cancer (NSCLC) remains the leading cause of cancer Bo Zhang1,2,* morbidity and mortality worldwide. In the present study, we identified novel biomarkers Yidan Sun3 associated with the pathogenesis of NSCLC aiming to provide new diagnostic and therapeu- Ran Xu1 tic approaches for NSCLC. Xinyi Hu4 Methods: The microarray datasets of GSE18842, GSE30219, GSE31210, GSE32863 and Shiqi Ren4 GSE40791 from Gene Expression Omnibus database were downloaded. The differential Qianqian Ma5 expressed genes (DEGs) between NSCLC and normal samples were identified by limma Chen Chen6 package. The construction of protein–protein interaction (PPI) network, module analysis and Jian Shu7 enrichment analysis were performed using bioinformatics tools. The expression and prog- Fuwei Qi7 nostic values of hub genes were validated by GEPIA database and real-time quantitative fi Ting He7 PCR. Based on these DEGs, the candidate small molecules for NSCLC were identi ed by the CMap database. Wei Wang2 Results: A total of 408 overlapping DEGs including 109 up-regulated and 296 down- Ziheng Wang2 regulated genes were identified; 300 nodes and 1283 interactions were obtained from the 1 Medical School of Nantong University, PPI network. The most significant biological process and pathway enrichment of DEGs were Nantong 226001, People’s Republic of China; 2The Hand Surgery Research Center, response to wounding and cell adhesion molecules, respectively. -
E2f8 Mediates Tumor Suppression in Postnatal Liver Development
Downloaded from http://www.jci.org on January 18, 2017. https://doi.org/10.1172/JCI85506 The Journal of Clinical Investigation RESEARCH ARTICLE E2f8 mediates tumor suppression in postnatal liver development Lindsey N. Kent,1,2,3 Jessica B. Rakijas,1,2,3 Shusil K. Pandit,4 Bart Westendorp,4 Hui-Zi Chen,1,2,3,5 Justin T. Huntington,1,2,3,6 Xing Tang,1,2,3 Sooin Bae,1,2,3 Arunima Srivastava,1,2,3,7 Shantibhusan Senapati,1,2,3 Christopher Koivisto,1,2,3 Chelsea K. Martin,1,2,3 Maria C. Cuitino,1,2,3 Miguel Perez,1,2,3 Julian M. Clouse,1,2,3 Veda Chokshi,1,2,3 Neelam Shinde,1,2,3 Raleigh Kladney,1,2,3 Daokun Sun,1,2,3 Antonio Perez-Castro,1,2,3 Ramadhan B. Matondo,4 Sathidpak Nantasanti,4 Michal Mokry,8 Kun Huang,9 Raghu Machiraju,7 Soledad Fernandez,9 Thomas J. Rosol,10 Vincenzo Coppola,1,3 Kamal S. Pohar,11 James M. Pipas,12 Carl R. Schmidt,6 Alain de Bruin,4,13 and Gustavo Leone1,2,3 1Department of Cancer Biology and Genetics, College of Medicine, 2Department of Molecular Genetics, College of Biological Sciences, and 3Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA. 4Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands. 5Division of Medical Oncology, Department of Internal Medicine, 6Department of Surgery, College of Medicine, and 7Department of Computer Science and Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, USA. 8Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands. -
Polycomb CBX7 Directly Controls Trimethylation of Histone H3 at Lysine 9 at the P16 Locus
Polycomb CBX7 Directly Controls Trimethylation of Histone H3 at Lysine 9 at the p16 Locus Qiang Li1., Xiuhong Wang1., Zheming Lu1, Baozhen Zhang1, Zhenpo Guan1, Zhaojun Liu1, Qiming Zhong1, Liankun Gu1, Jing Zhou1, Budong Zhu2, Jiafu Ji3, Dajun Deng1* 1 Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Etiology, Peking University Cancer Hospital and Institute, Beijing, China, 2 Department of Internal Medicine, Peking University Cancer Hospital and Institute, Beijing, China, 3 Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, China Abstract Background: H3K9 trimethylation (H3K9me3) and binding of PcG repressor complex-1 (PRC1) may play crucial roles in the epigenetic silencing of the p16 gene. However, the mechanism of the initiation of this trimethylation is unknown. Methodology/Principal Findings: In the present study, we found that upregulating the expression of PRC1 component Cbx7 in gastric cancer cell lines MGC803 and BGC823 led to significantly suppress the expression of genes within the p16- Arf-p15 locus. H3K9me3 formation was observed at the p16 promoter and Regulatory Domain (RD). CBX7 and SUV39H2 binding to these regions were also detectable in the CBX7-stably upregulated cells. CBX7-SUV39H2 complexes were observed within nucleus in bimolecular fluorescence complementation assay (BiFC). Mutations of the chromodomain or deletion of Pc-box abolished the CBX7-binding and H3K9me3 formation, and thus partially repressed the function of CBX7. SiRNA-knockdown of Suv39h2 blocked the repressive effect of CBX7 on p16 transcription. Moreover, we found that expression of CBX7 in gastric carcinoma tissues with p16 methylation was significantly lower than that in their corresponding normal tissues, which showed a negative correlation with transcription of p16 in gastric mucosa. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7
Article Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7 Graphical Abstract Authors N Kelsey N. Lamb, Daniel Bsteh, H O H O H O Sarah N. Dishman, ..., Lindsey I. James, N N N N N O O H O H O OH Oliver Bell, Stephen V. Frye Correspondence [email protected] (O.B.), [email protected] (S.V.F.) N H O H O H O N N N In Brief N N O O H O H O OH Lamb et al. describe the discovery of UNC4976 as a cellularly efficacious inhibitor of CBX7. Despite similar potency, selectivity, and permeability to previously published probe UNC3866, UNC4976 possesses a unique mechanism of action as a positive allosteric modulator of nucleic acid binding to CBX7 that rationalizes its enhanced cellular activity. Highlights d CBX7 mESC reporter line revealed UNC4976 as a more potent antagonist than UNC3866 d Unique mechanism of action for UNC4976 as a modulator of DNA/RNA binding to CBX7 d UNC4976 reduces CBX7/PRC1 CHIP peaks on chromatin with greater efficacy than UNC3866 d UNC4976 reactivates PRC1 target genes more effectively than UNC3866 in HEK293 cells Lamb et al., 2019, Cell Chemical Biology 26, 1–15 October 17, 2019 ª 2019 Elsevier Ltd. https://doi.org/10.1016/j.chembiol.2019.07.013 Please cite this article in press as: Lamb et al., Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7, Cell Chemical Biology (2019), https://doi.org/10.1016/j.chembiol.2019.07.013 Cell Chemical Biology Article Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7 Kelsey N. -
Anillin Is a Prognostic Factor and Is Correlated with Genovariation in Pancreatic Cancer Based on Databases Analysis
ONCOLOGY LETTERS 21: 107, 2021 Anillin is a prognostic factor and is correlated with genovariation in pancreatic cancer based on databases analysis YUANHUA NIE, ZHIQIANG ZHAO, MINXUE CHEN, FULIN MA, YONG FAN, YINGXIN KANG, BOXIONG KANG and CHEN WANG Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China Received March 12, 2020; Accepted October 8, 2020 DOI: 10.3892/ol.2020.12368 Abstract. Pancreatic cancer has a low survival rate globally. PC pathways were associated with low expression of ANLN. Anillin (ANLN) is involved in the pathogenesis of pancreatic Overall, ANLN is more highly expressed in PC compared cancer (PC). The present study used databases and reverse with in normal tissue, and is associated with poor differen‑ transcription‑quantitative PCR to investigate the association tiation. The expression of ANLN may be a novel prognostic between ANLN expression, clinical variables and the survival marker of poor survival. Finally, ANLN exert its functions in rate of patients with pancreatic cancer. Gene expression PC through the p53, cell cycle, DNA replication, mismatch of ANLN in normal and cancer tissues was analyzed using repair and nucleotide excision repair and pathways. data from The Cancer Genome Atlas, Oncomine and Gene Expression database of Normal and Tumor tissues 2 and Introduction ANOVA, and the association between ANLN mRNA expres‑ sion and ANLN genovariation was analyzed using cBioPortal. Pancreatic cancer (PC) is a major public health problem The association between ANLN expression and the survival, and is the eleventh most common cancer in the world, with clinical, pathological and prognostic characteristics of PC 458,918 new cases and 432,242 deaths in 2018 (1). -
Myopia in African Americans Is Significantly Linked to Chromosome 7P15.2-14.2
Genetics Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2 Claire L. Simpson,1,2,* Anthony M. Musolf,2,* Roberto Y. Cordero,1 Jennifer B. Cordero,1 Laura Portas,2 Federico Murgia,2 Deyana D. Lewis,2 Candace D. Middlebrooks,2 Elise B. Ciner,3 Joan E. Bailey-Wilson,1,† and Dwight Stambolian4,† 1Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States 2Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States 3The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States 4Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States Correspondence: Joan E. PURPOSE. The purpose of this study was to perform genetic linkage analysis and associ- Bailey-Wilson, NIH/NHGRI, 333 ation analysis on exome genotyping from highly aggregated African American families Cassell Drive, Suite 1200, Baltimore, with nonpathogenic myopia. African Americans are a particularly understudied popula- MD 21131, USA; tion with respect to myopia. [email protected]. METHODS. One hundred six African American families from the Philadelphia area with a CLS and AMM contributed equally to family history of myopia were genotyped using an Illumina ExomePlus array and merged this work and should be considered co-first authors. with previous microsatellite data. Myopia was initially measured in mean spherical equiv- JEB-W and DS contributed equally alent (MSE) and converted to a binary phenotype where individuals were identified as to this work and should be affected, unaffected, or unknown. -
Supplementary Data
SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche).